RetrogeneDB ID: | retro_pabe_3798 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | X:100548750..100550379(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PRKCI | ||
| Ensembl ID: | ENSPPYG00000014289 | ||
| Aliases: | None | ||
| Description: | protein kinase C iota type [Source:RefSeq peptide;Acc:NP_001126946] |
Retrocopy-Parental alignment summary:
>retro_pabe_3798
GAGACGTGTTCTTTTGACAACGAACAGCTCTTCACCATGAAATGGATAGACGAGGAAGGAGACCCGTGTACAGTATCATC
TCAGTTGGAGTTAGAAGAAGCCTTTAGACTTTATAAGCTAAACAAGGACTCTGAACTGTTGATTCATGTGTTCCCTTGTG
TACCAGAACGTCCCGGGATGCCTTGTCCAAGAGAAGATAAATCCATCTACCATAGAGGTGCATGCCGCTGGAGAAAGCTT
TATTGTGCCAATGGCCACACTTTCCAAGCCAAGCGCTTCAACAGGCGTGCTCACTGTGCCATCTGCACAGACCGAATATG
GGGACTTGGACGCCAAGGATATAAGTGCATCAACTTCAAACTCTTGGTTCATAAGAAGTGCCATAAACGCCTCACAATTG
AATGTGGGCGGCATTCTTTGCCACTGGAACAAATGATGCCCATGGATCAGTCATCCATGCATTCTGACCATGCACAGACA
GTAATTCCATATAATCCTTCAAGTCATGAGAGTTTGGATCAAGTTGGTGAAGAAAAAGAGGCAATGAACACCAGGGAAAG
TGGCAAAGCTTCATCCAGTCTAGGTCTTCAGGATTTTGATTTGCTCCGGGTAATAGGAAGAGGAAGTTAAGCCAAAGTAC
TGTTGGTTCCATTAAAAAAAAAAAAAAAGATCGTATTTATGCAATGAAAGTTGTGAAAAAAGAGCTTGTTAATGATGATG
AGGATATTGATTGGGTGCAGACAGAGACATATGTGTTTGAGTAGGCATCCAATCATCCTTTCCTTGTTGGGCTGCAGTGT
TGCTTTCAGACAGAAAGTAGATTGTTCTTTGTTATAGAGTATATAAATGGAGGAGACCTAATGTTTCATATGCAGCGACA
AAGAAAATTTCCTGAAGAACATGCCAGATTTTACTCTGCAGAAATCAGTCTAGCATTCAATTATCTTCATGAGCGAGGGA
TAATTTATAGAGATTTGAAACTGGACAATGTACTACTGGACTCTGAAGGCCACATTAAACTCACTGACTACGGCATGTGT
TAAGGAAGGATTACGGCCAGGAGATACAACCAGCACTTTCTGTGGTACTCCTAATTACATTGCTCCTGAAATTTTAAGAG
GAGGAGATTATGGTTTCAGTGTTGACTGGTGGGCTCTTGGAGTGCTAATGTTTGAGATGATGGCAGGAAAGTCTCCATTT
GATACTGTTGGGAGCTCCGATAACCCTGACCAGAACACAGAGGATTATCTCTTCCAAGTTATTTTGGAAAAACAAATTCG
CATACCACGTTCTCTGTCTGTAAAAGCTGCAAGTGTTCTGAAGAGTTTTCTTAACAAGGACCCTAAGGAATGATTGGGTT
GTCATCCTCAAACAGGATTTGCTGATATTCAGGGACACCCGTTCTTCTGAAATGTTGATTGGGATATGATGGAGCAAAAA
CAGGTAGTACTTCCCTTTAAAGCAAATATTTCTGGGGAATTTGGTTTGGACAACTTTGATTCTCAGCTTACTAATGAACC
TGTCCAGCTCACTCCAGATGTCGATGACATTGTGAGGAAGATTAATCAGTCTGAATTTGAAGGTTTTGAGTATATCAATC
CTCTTTTGATGTCTGCAGAAGAATGTGTC
ORF - retro_pabe_3798 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.38 % |
| Parental protein coverage: | 78.41 % |
| Number of stop codons detected: | 6 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | DMCSFDNEQLFTMKWIYDEGDPCTVSSQLELEEAFRLYELNKDSELLIHVFPCVPERPGMPCPGEDKSIY |
| ..CSFDNEQLFTMKWI..EGDPCTVSSQLELEEAFRLY.LNKDSELLIHVFPCVPERPGMPCP.EDKSIY | |
| Retrocopy | ETCSFDNEQLFTMKWIDEEGDPCTVSSQLELEEAFRLYKLNKDSELLIHVFPCVPERPGMPCPREDKSIY |
| Parental | RRGARRWRKLYCANGHTFQAKRFNRRAHCAICTDRIWGLGRQGYKCINCKLLVHKKCHKLVTIECGRHSL |
| .RGA.RWRKLYCANGHTFQAKRFNRRAHCAICTDRIWGLGRQGYKCIN.KLLVHKKCHK..TIECGRHSL | |
| Retrocopy | HRGACRWRKLYCANGHTFQAKRFNRRAHCAICTDRIWGLGRQGYKCINFKLLVHKKCHKRLTIECGRHSL |
| Parental | PPEPMMPMDQSSMHSDHAQTVIPYNPSSHESLDQVGEEKEAMNTRESGKASSSLGLQDFDLLRVIGRGSY |
| P.E.MMPMDQSSMHSDHAQTVIPYNPSSHESLDQVGEEKEAMNTRESGKASSSLGLQDFDLLRVIGRGS. | |
| Retrocopy | PLEQMMPMDQSSMHSDHAQTVIPYNPSSHESLDQVGEEKEAMNTRESGKASSSLGLQDFDLLRVIGRGS* |
| Parental | AKVLLVRLKKTDRIYAM--KVVKK-ELVNDDEDIDWVQTEKHVFEQASNHPFLVGLHSCFQTESRLFFVI |
| AKVLLV.......I..M..K..KK.ELVNDDEDIDWVQTE..VFE.ASNHPFLVGL..CFQTESRLFFVI | |
| Retrocopy | AKVLLVPXXXXXXIVFMQ*KL*KK<ELVNDDEDIDWVQTETYVFE*ASNHPFLVGLQCCFQTESRLFFVI |
| Parental | EYVNGGDLMFHMQRQRKLPEEHARFYSAEISLALNYLHERGIIYRDLKLDNVLLDSEGHIKLTDYGMC-K |
| EY.NGGDLMFHMQRQRK.PEEHARFYSAEISLA.NYLHERGIIYRDLKLDNVLLDSEGHIKLTDYGMC.K | |
| Retrocopy | EYINGGDLMFHMQRQRKFPEEHARFYSAEISLAFNYLHERGIIYRDLKLDNVLLDSEGHIKLTDYGMC>K |
| Parental | EGLRPGDTTSTFCGTPNYIAPEILRGEDYGFSVDWWALGVLMFEMMAGRSPFDIVGSSDNPDQNTEDYLF |
| EGLRPGDTTSTFCGTPNYIAPEILRG.DYGFSVDWWALGVLMFEMMAG.SPFD.VGSSDNPDQNTEDYLF | |
| Retrocopy | EGLRPGDTTSTFCGTPNYIAPEILRGGDYGFSVDWWALGVLMFEMMAGKSPFDTVGSSDNPDQNTEDYLF |
| Parental | QVILEKQIRIPRSLSVKAASVLKSFLNKDPKERLGCHPQTGFADIQGHPFFRNVDWDMMEQKQVVPPFKP |
| QVILEKQIRIPRSLSVKAASVLKSFLNKDPKE.LGCHPQTGFADIQGHPFF.NVDWDMMEQKQVV.PFK. | |
| Retrocopy | QVILEKQIRIPRSLSVKAASVLKSFLNKDPKE*LGCHPQTGFADIQGHPFF*NVDWDMMEQKQVVLPFKA |
| Parental | NISGEFGLDNFDSQFTNEPVQLTPDDDDIVRKIDQSEFEGFEYINPLLMSAEECV |
| NISGEFGLDNFDSQ.TNEPVQLTPD.DDIVRKI.QSEFEGFEYINPLLMSAEECV | |
| Retrocopy | NISGEFGLDNFDSQLTNEPVQLTPDVDDIVRKINQSEFEGFEYINPLLMSAEECV |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP007412_brain_prefrontal_cortex | 0 .39 RPM | 22 .95 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 20 .06 RPM |
| SRP007412_heart | 0 .09 RPM | 5 .66 RPM |
| SRP007412_kidney | 0 .17 RPM | 12 .50 RPM |
| SRP007412_liver | 0 .00 RPM | 4 .77 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3798 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3798 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_3798 has 2 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_4884 |
| Pan troglodytes | retro_ptro_3254 |
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000015212 | 1 retrocopy | |
| Homo sapiens | ENSG00000163558 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000014289 | 1 retrocopy |
retro_pabe_3798 ,
|
| Pan troglodytes | ENSPTRG00000015615 | 1 retrocopy |